[gmx-users] Why h_bond can not form

[范聪]

It's so kind of you to answer my question in such a short time. I'll try other forcefields. Thank you very much!
在 2015-05-11 19:46:27，Justin Lemkul <jalemkul at vt.edu> 写道：
>
>
>On 5/10/15 8:48 PM, 范聪 wrote:
>> Hello everyone!
>>
>> I offered a picture called "ask.png" to illistrate my question.
>>
>>   According to the referense papers, the H atom of the -OH group of TYR306 should form H_bond with the carbonyl O atom of the ligand.
>
>Depending on the methods used in those papers, maybe that hypothesis isn't right :)
>
>>   But in my simulations, the H atom turned after a very short time, towards the side chain of PHE152.
>> I guess the reason is that, first, the positive Zn ion near the ligand's carbonyl O atom made a repulsive effect against the H atom in -OH group; second, the π-electron cloud of the side chain of PHE attracted the H atom in the -OH group of TYR306.
>
>I wouldn't put any stock in any arguments about pi electron clouds in MD 
>simulations.  QM/MM shows clearly that the assignment of +2 charge to bound 
>metals is very crude and often a poor model of reality.
>
>>   As a whole, I failed to make out a real-enough simulation because the h_bond between the ligand and TYR306 did not form.
>>
>
>This could also be a force field issue, in general.
>
>>   Also I have one more question: Is there any tools or solutions to calculate the hydrophobic or π-π interactions between the ligand and seleted residues of the protein, so I could make a graph of the interactions against time?
>>
>
>You can map contacts, angles between the rings, etc.  See the manual for 
>available tools and discussions in the archive on these exact topics.
>
>-Justin
>
>-- 
>==================================================
>
>Justin A. Lemkul, Ph.D.
>Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
>Department of Pharmaceutical Sciences
>School of Pharmacy
>Health Sciences Facility II, Room 629
>University of Maryland, Baltimore
>20 Penn St.
>Baltimore, MD 21201
>
>jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>http://mackerell.umaryland.edu/~jalemkul
>
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